From elements to modules: regulatory evolution in Ascomycota fungi

https://doi.org/10.1016/j.gde.2009.09.007Get rights and content

Regulatory divergence is likely a major driving force in evolution. Comparative transcriptomics provides a new glimpse into the evolution of gene regulation. Ascomycota fungi are uniquely suited among eukaryotes for studies of regulatory evolution, because of broad phylogenetic scope, many sequenced genomes, and facility of genomic analysis. Here we review the substantial divergence in gene expression in Ascomycota and how this is reconciled with the modular organization of transcriptional networks. We show that flexibility and redundancy in both cis-regulation and trans-regulation can lead to changes from altered expression of single genes to wholesale rewiring of regulatory modules. Redundancy thus emerges as a major driving force facilitating expression divergence while preserving the coherent functional organization of a transcriptional response.

Introduction

The incredible diversity of living creatures defies their similarity in protein sequence and gene content. King and Wilson [1] first proposed that organismal diversity is likely driven by regulatory differences controlling when, where, and how genetic material is expressed. Nearly 35 years later, although examples of regulatory divergence are known in a wide range of species [2] including bacteria [3], fungi [4], flies [5], and mammals [6], the mechanisms through which regulatory systems evolve are still poorly understood. In recent years, comparative genomics approaches have allowed us to identify the functional components of genomes and to trace evolutionary events at different time scales [7, 8]. These approaches are also being used to infer the evolution of gene-expression regulation through two general approaches: characterization of cis-regulatory elements in orthologous promoter sequences, and comparative analysis of mRNA profiles across organisms. While studies relying on sequence data are more prevalent, functional studies of comparative gene regulation are now starting to shed light on how genome evolution is linked to functional changes.

Among eukaryotes, the Ascomycota fungi (Figure 1a) are particularly suitable for studies of eukaryotic regulatory evolution. More than 100 genome sequences exist for individual strains within Saccharomyces species and across fungi spanning hundreds of millions of years of evolution. They include model organisms (S. cerevisiae and S. pombe) and important human and agricultural pathogens (e.g. C. albicans, Aspergilli, and F. graminarium). Furthermore, sequenced genomes include species that diverged before and after a whole genome duplication (WGD, Figure 1a), which occurred ∼150 million years ago (mya) [9, 10]. This provides a unique opportunity to explore the effect of gene duplication on regulatory divergence. Finally, the relatively small (ca. 9–100 Mb) genomes are computationally tractable, but still display many of the hallmarks of eukaryotic gene regulation.

In this review, we focus on recent advances made in understanding the evolution of gene regulation in Ascomycota, from micro-evolutionary scales (<5 million years and typically within species) to macro-evolutionary time frames over tens of millions of years involving extensive speciation. (It is estimated that S. cerevisiae can undergo ∼2900 generations per year [11].) We examine conservation and divergence from two different perspectives: the regulation of mRNA expression at the level of single genes, and the coordinated expression of genes in regulons or ‘modules’ (i.e. sets of coregulated target genes) within a network. As we show, flexibility and apparent redundancy in gene copies, functional elements and molecular interactions may play a major role in driving the emergence of regulatory divergence, while conserving the functional backbone of transcriptional responses.

Section snippets

Functional and mechanistic corollaries of expression conservation and divergence

Available compendia of genome-wide mRNA profiles have allowed direct comparison of orthologous mRNA expression patterns across species. Large datasets exist for model Ascomycota (S. cerevisiae, S. pombe, and C. albicans), and smaller datasets are available for other fungi in the phylum (e.g. other sensu stricto Saccharomyces [12] C. glabrata [13], K. lactis [14], and some Euascomycota [15, 16]) as well as different strains within S. cerevisiae [12, 17, 18, 19, 20]. Together, these afford a

Gene duplication facilitates regulatory neo-functionalization

Gene duplication may provide a unique opportunity for ED of at least one of the two paralogs [29, 30, 31•]. In a comprehensive study of S. cerevisiae paralogs whose origins range to the last common ancestor with S. pombe (Figure 1a, root) we found surprisingly little divergence of the molecular function of paralogs, but substantial (∼70%) divergence in gene regulation, as reflected in the cis-regulatory elements, the transcription factors (TFs) bound to the genes’ promoters, and the gene

Flexibility in regulatory mechanisms can drive expression divergence

Genetic changes in both cis and trans elements can contribute to ED (Figure 1b). A genetic change can affect expression in cis, either directly by altering regulatory sequences controlling gene expression, or indirectly by modifying the activity of the gene's product and consequently affecting expression through feedback [35]. Polymorphisms in cis appear to contribute most to ED in phylogenetically close species, independent of environmental factors [22••]. Alternatively, a polymorphism distant

Expression divergence in transcriptional regulatory networks

It is challenging to reconcile the substantial evolutionary diversity in the expression of individual genes with the functional organization of regulatory networks. In particular, it is well established that transcriptional modules (regulons of coregulated genes) play a central role in regulatory networks [43, 44, 45]. Various modules are conserved across organisms from E. coli to humans [46, 47], including fungi [21]. However, if the regulation of individual genes is highly evolvable, how are

Conservation of regulatory modules over long evolutionary timeframes

Many regulatory modules are conserved across Ascomycota, often associated with conserved cis-regulatory elements and TFs (Figure 2a). Conserved modules can be identified by a statistically significant overlap in orthologous genes between modules of genes with correlated expression within each species [21, 48]. Alternatively, we can identify conserved regulation in gene modules [4] by comparing cis-regulatory elements enriched in the promoters of sets of orthologous coregulated genes.

Reshaping modules by gain and loss of gene targets

That orthologous regulatory modules can be detected over long time frames does not preclude substantial regulatory evolution. First, coexpression of genes in a module can collectively evolve simply by altering TF activation in response to different environmental cues and upstream signals. Second, cis-regulatory changes can drive gain and loss of targets to affect module composition, as well as regulatory patterns. Although the underlying mechanism is the same, the effects of target gain and

The role of redundancy in mediating regulatory rewiring of conserved modules

The formation of ‘seemingly redundant’ regulatory mechanisms may facilitate the dramatic rewiring of regulatory mechanisms while maintaining gene coregulation. In several cases, wholesale rewiring is observed between species diverged 200–300 mya, and appears to have been preceded by a period of redundant regulation on the order of 100–150 mya.

One prominent mode of redundancy is the formation of a module under the control of multiple regulatory systems, through distinct cis-regulatory sites (

Future prospects

While great advances have been made in the phenomenology and mechanistic understanding of the evolution of gene regulation, the relative roles of neutral drift and selective forces in promoting divergence remain largely unknown. For individual genes, purifying selection can be effectively invoked for the conservation of sites in closely related species, and for the low-ED of genes involved in growth processes. However, it is unclear how much of the increased divergence of high-ED genes is due

References and recommended reading

Papers of particular interest, published within the period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

Acknowledgements

The authors thank Sigrid Hart for graphics included in the figures. DJW was supported by an NLM training grant 5T15LM007359. DAT was supported by a Human Frontiers Science Program Research Grant. APG was supported by an NSF CAREER award (#0447887) and NIGMS R01GM083989-01. AR was supported by HHMI, by a Career Award at the Scientific Interface from the Burroughs Wellcome Fund, by an NIH Pioneer Award and by the Sloan Foundation.

References (67)

  • M. Kellis et al.

    Sequencing and comparison of yeast species to identify genes and regulatory elements

    Nature

    (2003)
  • P. Cliften

    Finding functional features in Saccharomyces genomes by phylogenetic footprinting

    Science

    (2003)
  • M. Kellis et al.

    Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae

    Nature

    (2004)
  • K.H. Wolfe et al.

    Molecular evidence for an ancient duplication of the entire yeast genome

    Nature

    (1997)
  • J. Fay et al.

    Evidence for domesticated and wild populations of Saccharomyces cerevisiae

    (2005)
  • I. Tirosh et al.

    A genetic signature of interspecies variations in gene expression

    Nat Genet

    (2006)
  • G. Lelandais et al.

    Genome adaptation to chemical stress: clues from comparative transcriptomics in Saccharomyces cerevisiae and Candida glabrata

    Genome Biol

    (2008)
  • A. Suleau et al.

    Transcriptomic analysis of extensive changes in metabolic regulation in Kluyveromyces lactis strains

    Eukaryot Cell

    (2006)
  • M.R. Andersen et al.

    A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species

    Proc Natl Acad Sci U S A

    (2008)
  • C. Tian et al.

    Transcriptional profiling of cross pathway control in Neurospora crassa and comparative analysis of the Gcn4 and CPC1 regulons

    Eukaryot Cell

    (2007)
  • R.B. Brem et al.

    Genetic dissection of transcriptional regulation in budding yeast

    Science

    (2002)
  • D.J. Kvitek et al.

    Variations in stress sensitivity and genomic expression in diverse S. cerevisiae isolates

    PLoS Genet

    (2008)
  • C.R. Landry et al.

    Genetic properties influencing the evolvability of gene expression

    Science

    (2007)
  • A. Tanay et al.

    Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast

    Proc Natl Acad Sci U S A

    (2005)
  • I. Tirosh et al.

    A yeast hybrid provides insight into the evolution of gene expression regulation

    Science

    (2009)
  • I. Tirosh et al.

    On the relation between promoter divergence and gene expression evolution

    Mol Syst Biol

    (2008)
  • J. Raser

    Control of sochasticity in eukaryotic gene expression

    Science

    (2004)
  • D. Wang et al.

    Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors

    Genome Res

    (2007)
  • I. Tirosh et al.

    Two strategies for gene regulation by promoter nucleosomes

    Genome Res

    (2008)
  • Y. Field et al.

    Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization

    Nat Genet

    (2009)
  • M. Vinces et al.

    Unstable tandem repeats in promoters confer transcriptional evolvability

    Science

    (2009)
  • Z. Gu et al.

    Duplicate genes increase gene expression diversity within and between species

    Nat Genet

    (2004)
  • Y. Guan et al.

    Functional analysis of gene duplications in Saccharomyces cerevisiae

    Genetics

    (2007)
  • Cited by (46)

    • Evolution of gene regulatory network of C<inf>4</inf> photosynthesis in the genus Flaveria reveals the evolutionary status of C<inf>3</inf>-C<inf>4</inf> intermediate species

      2023, Plant Communications
      Citation Excerpt :

      Compared with a single effector gene (e.g., enzyme) or regulatory gene (e.g., transcription factor [TF]), the GRN provides higher statistical robustness and biological interpretability in explaining the link between phenotype and genotype (Mitra et al., 2013). Therefore, comparative studies of GRNs across species will help dissect the novel network circuitry formed during the evolution of different taxa, enabling us to reconstruct the evolutionary pathway of phenotypes (Wohlbach et al., 2009; Romero et al., 2012; Necsulea and Kaessmann, 2014). C4 photosynthesis is a complex trait that evolved from the ancestral C3 type (Sage, 2004).

    • Inference and Evolutionary Analysis of Genome-Scale Regulatory Networks in Large Phylogenies

      2017, Cell Systems
      Citation Excerpt :

      Regulator-module associations change their sign between stresses, but these changes are rare and happen in a species- and clade-specific manner. A comparative framework for regulatory networks can provide insights into principles of gene regulation (Garfield and Wray, 2010; Li and Johnson, 2010; Wohlbach et al., 2009), as well as inform better learning of network structure (Penfold et al., 2015; Thompson et al., 2015). Here, we have presented our algorithm MRTLE for inferring regulatory networks for multiple species related by a known phylogeny.

    • Metabolic regulation in model ascomycetes - adjusting similar genomes to different lifestyles

      2015, Trends in Genetics
      Citation Excerpt :

      In this review we focus on recent examples of the differential regulation of metabolic networks in the ascomycetes, with an emphasis on the functionally divergent but genomically similar yeasts C. albicans and S. cerevisiae. This has been a fruitful area of recent investigation, and several aspects have been reviewed in the past few years, including the concept of rewiring of transcriptional circuits [3–5], differences in carbohydrate sensing [6], and the differential roles of post-translational modifications in cellular regulation [7]. The goal of such comparative studies is the description of how related organisms make unique use of their often similar genomes, a task that will require an understanding of the pressures that have led to these differences.

    • Saccharomyces diversity and evolution: A budding model genus

      2013, Trends in Genetics
      Citation Excerpt :

      S. cerevisiae is also becoming a leading model for population and quantitative genomics [3–6]. Comparisons to distant relatives continue to facilitate studies of evolutionary genomics [7], regulatory network evolution [8], and metabolic engineering [9]. In contrast to the numerous studies and reviews of variation within S. cerevisiae and comparisons to distantly related species, attempts to synthesize the progress toward understanding evolution within the Saccharomyces genus have been few [10].

    View all citing articles on Scopus
    *

    These authors contributed equally to this work.

    View full text